Mechanism of agonist-induced activation of the human itch receptor MRGPRX1

Mas-related G-protein-coupled receptors X1-X4 (MRGPRX1-X4) are 4 primate-specific receptors that are recently reported to be responsible for many biological processes, including itch sensation, pain transmission, and inflammatory reactions. MRGPRX1 is the first identified human MRGPR, and its expression is restricted to primary sensory neurons. Due to its dual roles in itch and pain signaling pathways, MRGPRX1 has been regarded as a promising target for itch remission and pain inhibition. Here, we reported a cryo-electron microscopy (cryo-EM) structure of Gq-coupled MRGPRX1 in complex with a synthetic agonist compound 16 in an active conformation at an overall resolution of 3.0 Å via a NanoBiT tethering strategy. Compound 16 is a new pain-relieving compound with high potency and selectivity to MRGPRX1 over other MRGPRXs and opioid receptor. MRGPRX1 was revealed to share common structural features of the Gq-mediated receptor activation mechanism of MRGPRX family members, but the variable residues in orthosteric pocket of MRGPRX1 exhibit the unique agonist recognition pattern, potentially facilitating to design MRGPRX1-specific modulators. Together with receptor activation and itch behavior evaluation assays, our study provides a structural snapshot to modify therapeutic molecules for itch relieving and analgesia targeting MRGPRX1.


Introduction
Itch is defined as the sensation that causes the desire to scratch the skin [1]. It is a common and frequently occurring symptom associated with many skin diseases among humans [2]. Numerous factors can induce itches, such as chemicals, insect bites, and even self-generated substances resulting from varied diseases [3]. Unfortunately, due to diverse inducements and complicated pathogenesis, treating itch in the clinic is still challenging, especially the chronic itch, which will devastate people and cause much suffering [4]. The itch can be generally divided into histaminergic and nonhistaminergic [5]. Usually, most histaminergic itch results a1111111111 a1111111111 a1111111111 a1111111111 a1111111111 in acute itch, whereas chronic itch is more probable to be nonhistaminergic [6]. Therefore, the well-developed antihistamine drugs are inefficient in chronic itch relieving, which suggests the significance of finding novel drug targets for chronic itch treatment [6].
Mas-related G-protein-coupled receptors (MRGPRs) have been recently identified as pruritogenic receptors mediating the nonhistaminergic itch [7]. The Mrgpr gene family encodes MRGPRs, a large family which comprises 27 and 8 members in mice and humans, respectively [7,8]. MRGPRX1-X4 are 4 primate-specific receptors, suggesting that the X subfamily may be a simplified alteration in human evolution [4]. MRGPRX1 is the first identified human MRGPR that expresses in dorsal root ganglia (DRG) and trigeminal ganglia (TG) specifically [4]. Compared with other MRGPRX members, MRGPRX1 stands out for its dual roles in mediating itch [9] and inhibiting persistent pain [10]. Persistent pain is a severe health problem worldwide, and ordinary analgesics like opioids targeting opioid receptors may lead to several side effects such as drug addiction [10,11]. Notably, MRGPRX1 is insensitive to the classical opioid receptor antagonists, indicating that MRGPRX1 could be a new target for treating chronic pain [10].
Extensive studies of MRGPRX1 were conducted in itch and pain sensations, and inflammation [7]. A series of natural and synthetic agonists, antagonists, and allosteric modulators of MRGPRX1 have been developed [12]. However, there is currently no drug targeting MRGPRX1 commercialized. The structure determination of GPCR may provide the detailed molecular basis of ligand interaction to facilitate modulator development [13]. Recently, 2 groups reported the agonist-stabilized cryo-electron microscopy (cryo-EM) structures of MRGPRX2 and MRGPRX4 in complexes with trimeric G proteins [14,15]. The structural characteristics of orthosteric pockets and modulator specificities are examined thoroughly. The critical acidic residues D184 5.38 and E164 4.60 in MRGPRX2 and the entirely positive orthosteric pocket in MRGPRX4 mainly determine the chemical property of varies modulators. The active structures of MRGPRX1 with varies of modulators are also reported [16].
In this study, we reported the cryo-EM structure of the active MRGPRX1-G q complex bound to compound 16 at an overall resolution of 3.0 Å. Compound 16 is a new synthetic MRGPRX1 agonist with high potency and selectivity over other MRGPRXs and opioid receptor [17]. Our complex structure reveals the conserved mechanism of small molecule-induced receptor activation among MRGPRX receptors. The structure also clearly presents a highly conserved orthosteric pocket for natural agonist recognition, such as bovine adrenal medulla 8-22 peptide (BAM8-22) [18], γ2-MSH [19,20], and conopeptide (CNF-Tx2) [21]. Notably, a few variable residues in orthosteric pocket of MRGPRX1 exhibit the unique agonist recognition pattern for compound 16. These findings will give us clues to the modification of small molecule scaffolds targeting MRGPRX1 specifically, potentially accelerating the development of novel drugs for the modulation of itch and pain.

The overall structure of G q -coupled MRGPRX1 bound to compound 16
To improve receptor expression, we fused thermostabilized apocytochrome b 562 (BRIL) [22] at the N-terminus of MRGPRX1. NanoBit tethering strategy [23] was used for the complex formation, with the LgBit and HiBit fused to the C-terminus of the receptor and G β subunit, respectively (S1A and S1B Fig). We used bioluminescence resonance energy transfer (BRET) assay to evaluate the impact of receptor modification on G protein coupling capability. The fusion of BRIL and LgBit to receptor only marginally affected receptor activity (S1C Fig and S1 Table). To further stabilize the complex, we used an engineered G αq chimera in the complex assembly. The engineered G αq chimera was designed based on the mini-G αs/q71 [24,25] with several modifications (S1D Fig). Briefly, the N-terminal 1-18 residues of the mini-G αs/q71 [24] were replaced by corresponding N-terminal sequences of the human G αi1 , while the α-helical domain of G αi1 was subsequently inserted into the mini-G αs/q71 , thus providing possible binding sites for 2 antibody fragments scFv16 and Fab-G50 [26,27]. Additionally, 2 dominant-negative mutations (G203A and A326S) were introduced to decrease the affinity of nucleotide binding [28]. The same engineered G αq chimera had been successfully used in the structure determination of several G q -bound GPCRs, including the G q -bound ghrelin receptor [29] and bradykinin receptors [30]. The engineered G αq chimera used in the further structure study will be simplified as G αq . We co-expressed BRIL-MRGPRX1-Lgbit, G αq , and G βγ -HiBit to obtain the MRGPRX1-G αq complex. The complex was further stabilized by incubating with Nb35 [31] and scFv16 [32] in the presence of compound 16 (S2 Fig).
The compound 16-MRGPRX1-G αq complex structure was determined by cryo-EM to yield a final map at an overall resolution of 3.0 Å (Figs 1A and S3A-S3F and S2 Table). In the map, the densities for the receptor, G αq , G βγ , Nb35, scFv16, and compound 16 could be well distinguished, and the interface residues between MRGPRX1 and G αq (α5-helix) were clearly defined (S3G Fig). Thus, we built a reliable atomic model based on the well-traced α-helices and aromatic side chains (Fig 1B). Due to the flexibility, the N-terminus (M1-K25), part of the extracellular loops (I90) and long C-terminal residues (R279-Q322) of the receptor are invisible.

The orthosteric pocket of MRGPRX1
The MRGPRX1 exhibits a shallow, broad, and wide-open ligand-binding pocket (Fig 2A). The distance between compound 16 and the critical toggle switch residue G229 6.48 is about 16.8 Å (Fig 2B), indicating that compound 16 is positioned near the extracellular surface but not buried deep in the receptor. The shallow pockets are also observed in the MRGPRX2-G αq [14,15] and MRGPRX4-G αq complex [14], suggesting the common pocket features among all MRGPRX receptors. Compound 16 occupies only about one-third of the pocket (Fig 2A) but  The electrostatic potential of the MRGPRX1 pocket is partially negative, partially positive, and partially hydrophobic (S4D Fig). In contrast, the electrostatic potential of the MRGPRX2 pocket is partially negative (sub-pocket 1) and partially hydrophobic (sub-pocket 2), and the electrostatic potential of MRGPRX4 pocket is positive (S4E and S4F Fig). These results suggest that MRGPRXs may prefer agonist scaffolds with distinct electro-properties.
The orthosteric pocket of MRGPRX1 accommodating compound 16 is composed of residues majorly located on TM3/4/5/6 ( Fig 2C). C161 4.64 and C173 5.32 form a disulfide bond, which is conserved among MRGPRXs [14] (S5 Fig). Moreover, alanine substitutions of C161 4.64 and C173 5.32 nearly abolish the G q coupling activity ( Fig 2D). Interestingly, MRGPRX1 lacks the canonical disulfide bond between TM3 and ECL2 in other class A family GPCRs [33]. Taken together, the disulfide bond substitution in MRGPRX1 may help to reorganize the extracellular loops and maintain the wide-open orthosteric pocket.

The interaction between compound 16 and MRGPRX1
Compound 16 adopts a hairpin conformation in the pocket due to the intramolecular π-π interaction of the 1-aminoisoquinoline and phenylmethyl groups ( Fig 1A). Notably, the amino group of 1-aminoisoquinoline forms strong salt bridges with E157 4.60 and D177 5.36 ( Fig Table). Additionally, the variable residue Y99 3.29 recognizes compound 16 through 2 types of interactions, the π-π interaction with the middle aromatic ring of compound 16 and polar interaction with the amino group of 1-aminoisoquinoline (Fig 2E and 2F). Alanine substitution of Y99 3.29 nearly abolishes the G q coupling activity (Figs 2G and S6 and S1 Table). Thus, the variable residue Y99 3.29 is essential for recognizing compound 16. Besides, the positive charge residue K96 3.26 in MRGPRX1 is conserved in MRGPRX4 but substituted by a serine in MRGPRX2 (S5 Fig). K96 3.26 in MRGPRX1 is close to compound 16 ( Fig 2E and 2F), but S103 3.26 in MRGPRX2 is far away from (R)-ZINC-3573 (S7A Fig). However, the alanine substitution of K96 3.26 slightly affects the receptor activation (Figs 2G and S6 and S1 Table), suggesting that K96 3.26 does not directly participate in compound 16 recognition. In contrast, the K96 3.26 in MRGPRX4 is critical for MS47134 recognition [14] (S7B Fig). The variation of pocket residues may partly explain the agonist selectivity among MRGPRXs [12]. Apart from these closer residues, the farther hydrophobic residues around compound 16, such as W158 4.61 , F236 6.55 , F237 6.56 , L240 6.59 , and W241 6.60 , also participate in the ligand-binding pocket formation (Fig 2E and 2F). These hydrophobic residues, except for F237 6.56 , exhibit indirect and relatively weak interactions with compound 16 (Figs 2H and S6 and S1 Table). Alanine mutation of F237 6.56 shows a notable impact on compound 16-induced MRGPRX1 activation (Figs 2H and S6 and S1 Table), indicating a potentially crucial role of F237 6.56 in ligand recognition or receptor activation. However, the alanine substitution of F236 6.55 only partially affects the receptor activation, double confirmed by BRET assay and calcium imaging assay (Figs 2H and S6 and S1 Table). It suggests that F236 6.55 may help maintain the ligand-binding pocket instead of directly interacting with the ligand. Besides, the activity of compound 16 is partially reduced by substituting L240 6.59 with alanine in the BRET assay ( Fig 2H and S1 Table). In contrast, it is not affected in the calcium imaging assay (S6 Fig). The discrepancy may indicate L240 6.59 is less important for

Activation of MRGPRX1
The compound 16-MRGPRX1-G αq complex structure exhibited TM rearrangement in the cytoplasmic half. The cytoplasmic ends of TM3 and TM6 are about 16 angstroms apart, consistent with other class A G protein-engaged GPCRs in an active conformation [33] (Fig 3A). Notably, the conserved toggle switch W 6.48 in other GPCRs is replaced by G229 6.48 in MRGPRX1. This vital substitution results in an inward movement of the extracellular half of TM6, narrowing the gap between TM3 and TM6 and initiating the formation of a shallow orthosteric pocket ( Fig 3B). Briefly, Y106 3.36 in TM3 engages with G229 6.48 in TM6 to form a twist. This twist is then stabilized by the hydrophobic interactions network among Y106 3.36 , F232 6.51 , and F237 6.56 , which prevents the ligands from entering the deeper location and exhibits a shallow pocket to accommodate ligands. Additionally, we conducted a structural comparison of MRGPRX1 complex to its functional closely related μ opioid receptor (μOR) in the active state (PDB 7U2L) [34] and inactive state (PDB 7UL4) [35] (Fig 3C). The structural comparison demonstrates that the MRGPRX1 complex shows a similar structure as the active μOR. Moreover, the structure superposition of G αq -coupled MRGPRX1 with G αq -coupled 5-HT 2A R (PDB 6WHA) [36] and G αq -coupled B1R (PDB 7EIB) [30] by receptors also exhibits similar conformations (S8A and S8B Fig), suggesting a common activation mechanism among these receptors. Significantly, except for the extracellular half of TM6, G αq -coupled MRGPRX1 shows nearly identical conformations of TM3, TM6, and TM7 with these receptors in active state (Figs 3C and S8). MRGPRX1 possesses several unique residues in its extracellular half of TM6, which are essential for receptor activation. Furthermore, consistent with our speculation, alanine mutations of these residues dramatically affected MRGPRX1 activation induced by compound 16 (Fig 3D). Hence, the initiation of MRGPRX1 activation is likely triggered by touching F237 6.56 at the bottom of the pocket upon agonist binding, pushing a series of residues in TM6 to move towards TM3 and resulting in the conformational change of G229 6.48 . G229 6.48 shifts to get close to Y106 3.36 , triggers the rotation of conserved F 6.44 , and further facilitates the intracellular half of TM6 moving outward to accommodate the downstream G protein (Figs 3C and S8).
In addition to the unique twist structure in TM6, MRGPRX1 also shows significant differences in some classic motifs for class A GPCR activation. Firstly, the conserved D (E) 3.49 R 3.50 Y 3.51 motif on TM3 of most class A GPCRs forms an ionic lock in an inactive conformation and is broken upon activation [33]. In MRGPRX1, Y 3.51 is replaced by C121 3.51 , E119 3.49 interacts with R134 ICL2 via a strong salt bridge, and R120 3.50 interacts with T217 6.36 to near the substituted toggle switch G229 6.48 . (C) Structural superposition of active MRGPRX1, active μOR (PDB 7U2L) [34] and inactive μOR (PDB 7UL4) [35] from the side, cytoplasmic, and magnified views. The movement directions of TM6, TM7, and residues in MRGPRX1 relative to inactive μOR are highlighted as red arrows. MRGPRX1, active μOR, and inactive μOR are colored in slate, light pink, and gray, respectively. (D) BRET validation of essential residues in the extracellular half of TM6. Data are presented as mean ± SEM. n = 3; Emax, maximum effect; WT, wild type. Magnified view of D/ERY motif (E), LLLF motif (F), and NPXXY motif (G). Polar interactions are shown as yellow dashed lines. The underlying data for Fig 3D can be found in S1 Data. BRET, bioluminescence resonance energy transfer; μOR, μ opioid receptor.

The coupling of G αq to MRGPRX1
The coupling of G αq to MRGPRX1 is mainly maintained by interacting with residues on TM2, TM3, TM5, TM6, and ICL2 (S9A Fig). The interface between G αq and TMs comprises a series of hydrophobic residues, including F61 2.39 , V124 3.54 , I202 5.61 , L211 6.30 , and L214 6.33 on the receptor and L352, L356, and L361 on the α5-helix of G αq (S9B Fig). However, alanine substitutions of these hydrophobic residues have little effect on G αq coupling activity (S9C Fig and S1 Table). Only I202 5.61 A partially reduces G αq activation (S9C Fig and S1 Table), suggesting that the TM bundles are less critical for G αq activation in MRGPRX1. Moreover, in most class A GPCRs, ICL2 does not interact with G protein directly. However, extensive interactions of ICL2 with the αN-helix and α5-helix of G αq are observed in the MRGPRX1 structure (S9D Fig). Alanine substitutions of I128 ICL2 and H133 ICL2 nearly impair G αq coupling activity (S9E and S9F Fig, S1 Table), indicating that ICL2 plays a crucial role in G αq coupling. Similar G protein coupling interfaces are also observed in the complex structures of MRGPRX2 and MRGPRX4 previously reported (S10A and S10B Fig).

Discussion
In this study, we used the NanoBiT strategy to determine the structure of compound 16-bound MRGPRX1 in complex with G αq via cryo-EM. We compared our compound 16-MRGPRX1-G αq complex structure to the recently reported MRGPRX1-G αq complex structure contributed by Liu and colleagues [16]. The overall structures are similar (S11A Fig), but the significant difference is the orientation of the phenylmethyl group in compound 16 (S11B and S11C Fig). Due to the better ligand density in our structure, compound 16 could be accommodated well with our proposed conformation. In contrast, the ligand leaves a part of the phenyl group out of the density map when we use Liu's structure to fit the density. Our structure reveals the common feature of shallow, broad, and wide-open orthosteric pockets in all MRGPRX members. We speculated that this shallow and broad pocket might easily accommodate various small compounds with distinct scaffolds. The less selectivity helps the receptor expand the ligand spectrum of itch sensation and facilitates the body's quick response to the diverse exogenous stimulus.
Notably, the binding site of compound 16 is closed to TM3 and TM4 of MRGPRX1, while the binding site of (R)-ZINC-3573 is closed to TM5 and TM6 of MRGPRX2 (Figs 2C and S12A). The conformation of ECL2 in MRGPRX2 may prevent the ligand access to the corresponding position in MRGPRX1 (S12B Fig). Similarly, the binding site of MS47134 is closed to TM2 and TM3 of MRGPRX4 (S12C Fig). The inward movement of TM3, TM4, and ECL2 in MRGPRX4 may prevent the ligand access to the corresponding position in MRGPRX1 (S12D Fig). Due to the distinct binding regions and the orthosteric pocket differences of these receptors, we evaluated the activation of compound 16 on MRGPRXs. As a result, MRGPRX1 is the only receptor that can be significantly activated by compound 16 with high potency (Figs 4A and S13A-S13I). All the above further confirms that the MRGPRXs differ in ligand recognition. Together with the highly conserved G protein interfaces among MRGPRXs, it can be concluded that MRGPRXs are activated by different ligands but use a general approach to recruit G proteins. These structural differences provide clues to design agonists with improved specificity and potency.
Moreover, MRGPRX1 reportedly involves in itch sensation [9] and pain inhibition [10]. Chloroquine (CQ), a drug widely used in malaria treatment, can cause itch in some people [38][39][40]. It is recently reported that MRGPRX1 mediates CQ-induced itch in humans [40]. Compound 16 was designed to inhibit chronic pain by targeting MRGPRX1. It is more abundant in the spinal cord than in the circulatory system, suggesting a lower risk of side effects caused by unexpected activation of MRGPRX1 [17]. Given its high potency, high selectivity, and restricted distribution, compound 16 is a viable candidate drug worthy of more attention and further study [17]. Accordingly, we tested the severity of itching that compound 16 might induce to evaluate whether the itch side effects would limit its application. Here, we used the scratching responses on the mouse model to evaluate the itch severity of compound 16 and CQ. Resultedly, compound 16 induces much less itch than a similar quantity of CQ (200 μg) (Fig 4B). To further investigate why compound 16 behaved differently than CQ, we tested the activation effect of compound 16 on MrgprA3 and MrgprC11, both the mouse orthologs of human MRGPRX1. Notably, MrgprA3 was found to be the main receptor mediating CQ-evoked responses in mice [40]. Our results showed that compound 16 could not activate MrgprA3 or MrgprC11 even at the concentration of 500 μM (Figs 4C and 4D and S13L and S13M). In other words, compound 16 failed to act as an agonist of mouse MrgprA3 and MrgprC11 but is a specific human MRGPRX1 agonist. Conversely, CQ shows higher potency to MrgprA3 (EC 50 : 27.55 μM) than MRGPRX1 (EC 50 : 297.68 μM) [40].
Determination of high-resolution CQ-bound MRGPRX1 and MrgprA3 structures may help us decipher the molecular basis of ligand recognition specificity. However, it is challenging to get a CQ-bound MRGPRX1 structure due to its low efficacy. Here, we performed molecular docking to analyze the recognition difference between MRGPRX1 and MrgprA3 for CQ (S14A and S14B Fig). The model of activated MrgprA3 was generated using MRGPRX1 as a template. Results show that CQ occupies a position away from TM6 in the binding pocket of MRGPRX1 compared with compound 16 in the MRGPRX1-compound 16 complex structure. It shows that the interactions between CQ and critical hydrophobic residues (F236 6.55 , F237 6.56 , and L240 6.59 ) in TM6 are weaker than in compound 16. We speculate that CQ weakly activates MRGPRX1 due to its weak interactions with critical hydrophobic residues in TM6. Interestingly, the 7-chloroquinolin group of CQ in the pocket of MrgprA3 gets closer to TM6 when compared with that in MRGPRX1 structure. It is consistent with our speculation that stronger interactions with critical hydrophobic residues in TM6 will improve the ligand-binding affinity. Meanwhile, we also noticed several amino acids in the ligand-binding pocket that are unconserved between MRGPRX1 and MrgprA3. This may induce the different binding pose and affinity for compound 16 and CQ between MRGPRX1 and MrgprA3. Y99 3.29 in MRGPRX1, critical for compound 16 binding, is replaced by a histidine in MrgprA3, which may affect the activation of MrgprA3 by compound 16. Furthermore, studies on the downstream effectors of MRGPRX1, especially transient receptor potential vanilloid 1 (TRPV1) and transient receptor potential ankyrin 1 (TRPA1), show some conflicts. TRPV1 is usually regarded as an ion channel involved in pain sensation [41]. Wilson and colleagues found that TRPA1 is required for CQ-induced mice itch mediated by MrgprA3 [42]. The tick salivary peptide IPDef1 has been reported to evoke mice itch via MrgprC11 and result in the activation of the downstream ion channel TRPV1 rather than TRPA1 [43]. These data are consistent with the overlap between itch-sensing pathways and pain-sensing pathways. Thus, the differences in downstream signaling of MRGPRX1-mediated pain and itch sensations still need further investigation.

Construct design
The full-length wild-type (WT) human MRGPRX1 (residues M1-S382) was cloned into pFast-Bac vector with an HA signal peptide, an N-terminal Flag tag, and a C-terminal 10×His tag. A BRIL [22] protein was fused at the N-terminus of MRGPRX1 to improve the expression of the receptor. LgBit [23] was fused at the C-terminus of MRGPRX1 to stabilize the whole MRGPRX1-Gαq complex. There was no more modification for the MRGPRX1 sequence. Prof. H. Eric Xu from Shanghai Institute of Materia Medica donated the engineered Gαq chimera plasmid. This engineered G αq [29,30] was designed based on a mini-G αs/q71 [24,25] skeleton with the replacement of G i1 N-terminus and the insertion of G αi1 α-helical domain, thus providing possible binding sites for 2 antibody fragments scFv16 and Fab-G50 [26,27]. Additionally, 2 dominant-negative mutations (G203A and A326S) were introduced to decrease the affinity of nucleotide binding [28]. The WT G β1γ2 with HiBit [23] fused at the C-terminus of the β1 subunit was cloned into pFastBac-Dual vector. Ric8A is a molecular chaperone that has been reported to be essential for the biogenesis and signaling of G αq subunits, and the involved functions include facilitating the proper folding of G αq and promoting the formation of G α guanine nucleotide-binding pocket [44][45][46]. The full-length Ric8A was cloned into pFastBac vector. For biochemical assay, the full-length WT MRGPRX1 and the MRGPRX1 point mutants were cloned into mammalian expression vector pCDNA 3.1 with an N-terminal Flag tag. All these constructs were generated with a standard PCR-based strategy and homologous recombination (CloneExpress One Step Cloning Kit, Vazyme).

Expression and purification of scFv16
The scFv16 with a C-terminal 8×His tag was expressed in Trichoplusia ni Hi5 insect cells and purified precisely as previously described [26,32,47]. Briefly, the Hi5 insect cells (3.0 to 4.0 million cells per mL) were infected with the scFv16 virus produced by the Bac-to-Bac system (Invitrogen) for 96 h. Then, the medium was collected and pH balanced to pH 8.0 by adding Tris-base powder. Chelating agents were quenched by adding 1 mM nickel chloride and 5 mM calcium chloride. After incubation at room temperature (25˚C) for 1 h by stirring constantly, the supernatant was isolated by centrifugation (4,750 rpm, 30 min, 4˚C) and incubated with Ni-sepharose (GE Healthcare) for 1 h at room temperature with constant stirring. The resin was collected and then washed by washing buffer (20 mM HEPES (pH7.5), 100 mM NaCl, and 20 mM Imidazole). The protein was eluted by elution buffer (20 mM HEPES (pH 7.5), 100 mM NaCl, and 250 mM Imidazole) and then incubated with HRV-3C protease at 4˚C for 2 h to remove the C-terminal 8×His tag. The cleaved protein was further loaded onto Superdex 200 Increase 10/300 GL column (GE Healthcare) with running buffer (20 mM HEPES (pH 7.5), 100 mM NaCl). ScFv16 peak fraction was collected, flash-frozen, and stored at −80˚C until use.

Expression and purification of Nb35
Nanobody-35 (Nb35) was expressed in the Escherichia coli BL21 (DE3) and purified as previously reported [30,31]. Nb35 was cultured in LB with 50 μg/mL ampicillin at 37˚C, 220 rpm for about 3 h until OD 600 reached 1.0. Then, IPTG was added to induce the protein expression at 25˚C, 220 rpm with a final concentration 1 mM. Then, the E. coli bacteria were collected by centrifugation (4,000 rpm, 20 min, 4˚C) after 16 h. The pellets were resuspended in lysis buffer (25 mM HEPES (pH 7.5), 150 mM NaCl, 1 mM PMSF) and disrupted by ultrasonication. The supernatant was isolated by centrifugation (14,000 rpm, 60 min, 4˚C) and incubated with Ni-NTA resin (Qiagen) for 1 h. The resin was washed by washing buffer (25 mM HEPES (pH 7.5), 150 mM NaCl, and 25 mM Imidazole) and then eluted by elution buffer (25 mM HEPES (pH 7.5), 150 mM NaCl, and 250 mM Imidazole). The eluted protein was concentrated and loaded onto Superdex 200 Increase 10/300 GL column (GE Healthcare) with running buffer (25 mM HEPES (pH 7.5), 150 mM NaCl). The Nb35 monomeric fractions were pooled and stored at −80˚C for further use.

Cryo-EM sample preparation and data acquisition
The concentrated sample (3.5 μL) at a concentration of 12 mg/mL was applied to glow-discharged holey carbon-coated grids (Quantifoil 200 mesh, Au R1.2/1.3). The grids were blotted for 3.5 s and flash-frozen in liquid ethane using a Vitrobot (Mark IV, Thermo Fisher Scientific). Images were recorded on a 300 kV Titan Krios G3i electron microscope (Thermo Fisher Scientific) equipped with Gatan K3 Summit direct detector and a GIF Quantum energy filter (slit width 20 eV). Movie stacks were collected using SerialEM [48] in counting mode at a magnification of 105,000× with the corresponding pixel size of 0.85 Å. Movies stacked with 50 frames were exposed for 2 s. Two data sets of the same sample were collected, including 3,447 and 2,799 movies separately. Two data sets were recorded at a total dose of about 56.15 e/Å2 and 58.32 e/Å2, respectively. The defocus range was set from −1.0 μM to −2.0 μM.

Data processing
Data processing was performed using cryoSPARC [49]. Movies frames were aligned using Patch motion. CTF estimation was performed using Patch CTF. Particles were first picked using a blob picker with partial micrographs. 2D templates were generated by 2D classification. Particle picking of all micrographs was performed by a template picker. A total of 6,687,388 particles from 6,246 micrographs were extracted using a box size of 288 pixels and cropped into 72 pixels. After 2 rounds of 2D classification and 1 round of ab initio reconstruction, 1,808,631 particles were selected and re-extracted using a box size of 288 pixels. Ab initio reconstruction using partial particles was performed, and 279,237 particles were removed, remaining 1,529,394 particles. After that, 1 round of nonuniform and local refinement was performed. One round of ab initio reconstruction was performed again, generating a new data set with 1,006,848 particles. Finally, 1 round of nonuniform and local refinement was performed, generating a 3.0 Å map.

Model building and refinement
The initial complex model was built using the structure of MRGPRX2 (PDB code: 7S8N) and Nb35 (PDB code: 7F4H) as templates. Models are then fitted into the density map and manually adjusted and rebuilt in COOT [50]. The restraint files of compound 16 and CHS were generated by Phenix.elbow package [51]. The complete model was finally refined in Phenix using real-space refinement with secondary structure and geometry restraints [52] and COOT. Overfitting of the model was checked by refining the model using one of the 2 independent maps from gold-standard refinement and calculating FSC against both half maps [53]. The final model was validated using Molprobity [54] (S2 Table). Structural figures were prepared in PyMOL (https://pymol.org/2/), UCSF Chimera [55], and UCSF ChimeraX [56].

Behavioral studies
WT C57BL/6J mice (8-week-old males) in acute itch behavioral tests were purchased from the Disease Control and Prevention Center of Hubei Province in China. Vehicle and MRGPRX1 agonists were subcutaneously injected into the nape of neck of mice after acclimatization. Scratching behavior in mice was observed for 30 min following injection. A bout of scratching was defined as a scratching movement with the hind paw directed at the area of the injection site. Then, the scratching bouts directing at the injected site were quantified.

Ethics statement
All acute itch behavioral tests in mice were performed with subcutaneous injection of compounds and approved by the Animal Care and Ethical Committee of Wuhan University under the International Association for the Study of Itch guidelines (Approval number: WDSKY0201707-2). After itch experiments, all mice were humanely killedAU : PleasenotethatasperPLO by carbon dioxide asphyxiation.

Molecular docking
Molecular docking was performed using AutoDock Vina [58,59]. Briefly, the structure of MRGPRX1-compound 16 and the model of MrgprA3 using homology modeling based on the structure of MRGPRX1-compound 16 were used to do CQ docking. Homology modeling of MrgprA3 was performed using Swiss-model [60,61]. Open Babel was used to prepare the coordinates file of CQ and receptor with polar-hydrogens. A grid box with 25 × 25 × 25 grid points was used for searching. The results were checked, and the 2 top-ranking binding poses were selected. Figures were prepared in PyMOL (https://pymol.org/2/). Supporting information S1 Fig. Construct for MRGPRX1, G β -HiBit,  (B) A comparison between MRGPRX1-compound 16 and docking MrgprA3 structure with CQ. Key residues and ligands are shown as sticks. MRGPRX1, docking MRGPRX1, and MrgprA3 are colored slate, pale green, and gray, respectively. Compound 16 and CQ are colored cyan and hot pink, respectively. (TIF) S15 Fig. Raw data of the BRET assay. Dose-response curves comparison of WT with ligandbinding pocket residues (A), G αq interface residues (B), and MRGPRXs (C). Data are presented as mean ± SEM. n = 3; WT, wild type. The underlying data for S15A-S15C Fig can be found in S1 Data. (TIF) S1 Table. Statistics of BRET assay for MRGPRX1 mutants. (PDF) S2 Table. Cryo-EM data collection, refinement and validation statistics. (PDF) S1 Data. Underlying data for Figs 2D, 2G, 2H, 3D, 4A-4D, S1C, S2B, S9C, S9E, S9F, S13I-S13M and S15A-S15C.